Glossary

Glossary of Terms

Table 1: General terms

Abundance	The quantity or concentration of a specific cell type or marker within a sample, measured per individual .fcs file. Often used to describe the relative or absolute presence of cell populations in cytometry.
cluster	Pre-defined groups of similar cells based on specific characteristics or measurements, used to analyze subsets within cytometry data. Clusters are identified prior to analysis in the app.
Differential Abundance	The comparison of abundance levels between different conditions or groups in cytometry data to identify significant changes in cell populations.
Differential State	Refers to the analysis of changes in state or condition of cell populations under different experimental conditions, assessing variations beyond mere abundance. Calculates tests for differential states within cell populations (i.e. differential expression of cell state markers within clusters).
FCS	Fluorescence-activated Cell Sorting file, a data format that contains information about each individual cell measured.
Gating	Method used to select cells based on specific criteria, allowing for the analysis of cell subpopulations. Gating is performed prior to data analysis in the app.
Metadata
MFI	Mean Fluorescence Intensity, a measure to quantify the average fluorescence intensity of cells within a gated population, indicative of protein expression levels.
State Markers	Indicators used in cytometry to identify transient or conditional characteristics of cells, such as activation or stress responses, reflecting the dynamic states of cells.
Type Markers	Specific markers used in cytometry to classify cells into distinct types or classes based on their inherent properties, such as cell lineage or functional attributes.

Table 2: Bioinformatic terms

count	Number of cells per .fcs in each clusters.
perCellCounts	Frequencies of cells, expressed as abundances per individual cell, allowing for comparison across samples with varying total cell counts.
perCellCountsNorm	Frequencies normalized using the arcsinh transformation (scaled by 0.03) and then centered by the mean per cluster/gating. Commonly used to stabilize variance across a range of values.
SummarizedExperiment	A class in R used to store experimental data along with annotations about the experiments. It encapsulates data in a way that retains the relationship between data and metadata, useful for complex analyses.
SingleCellExperiment	A specialized version of SummarizedExperiment designed specifically for cell-level data. It facilitates the handling of single-cell specific metrics and annotations.